.. _publications_about_neuron:

Publications about NEURON
=========================

Awile, O., Kumbhar, P., Cornu, N., Dura-Bernal, S., King, J. G., Lupton, O., Magkanaris, I., McDougal, R. A., Newton, A. J. H., Pereira, F., Săvulescu, A., Carnevale, N. T., Lytton, W. W., Hines, M. L., Schürmann, F. (2022). Modernizing the NEURON Simulator for Sustainability, Portability, and Performance. *bioRxiv*. `doi:10.1101/2022.03.03.482816 <https://doi.org/10.1101/2022.03.03.482816>`_

McDougal, R. A., Conte, C., Eggleston, L., Newton, A. J. H., Galijasevic, H. (2022). Efficient simulation of 3D reaction-diffusion in models of neurons and networks. *bioRxiv*. `doi:10.1101/2022.01.01.474683 <https://doi.org/10.1101/2022.01.01.474683>`_

Hines M., Carnevale T., McDougal R.A. NEURON Simulation Environment (2019). In: Jaeger D., Jung R. (eds) *Encyclopedia of Computational Neuroscience*. Springer, New York, NY. `doi:10.1007/978-1-4614-7320-6_795-2 <https://doi.org/10.1007/978-1-4614-7320-6_795-2>`_

Newton, A. J., McDougal, R. A., Hines, M. L., Lytton, W. W. (2018). 
Using NEURON for Reaction-Diffusion modeling of extracellular dynamics.
*Frontiers in Neuroinformatics*, 12, 41. 
`doi:10.3389/fninf.2018.00041 <https://doi.org/10.3389/fninf.2018.00041>`_

Lytton, W. W., Seidenstein, A. H., Dura-Bernal, S., McDougal, R. A., Schürmann, F., Hines, M. L. (2016). Simulation neurotechnologies for advancing brain research: parallelizing large networks in NEURON. *Neural computation*, 28(10), 2063-2090.

McDougal RA, Hines ML, Lytton WW. Reaction-diffusion in the NEURON simulator (2013). *Frontiers in Neuroinformatics*. 7:28. `doi:10.3389/fninf.2013.00028 <https://doi.org/10.3389/fninf.2013.00028>`_

Hines, M., Kumar, S., Schürmann, F. (2011). Comparison of neuronal spike exchange methods on a Blue Gene/P supercomputer. *Frontiers in computational neuroscience*, 5, 49. `doi:10.3389/fncom.2011.00049 <https://doi.org/10.3389/fncom.2011.00049>`_

Kumar, S., Heidelberger, P., Chen, D., Hines, M. (2010). Optimization of applications with non-blocking neighborhood collectives via multisends on the blue gene/p supercomputer. In 2010 IEEE International Symposium on Parallel & Distributed Processing (IPDPS) (pp. 1-11). IEEE. `doi:10.1109/IPDPS.2010.5470407 <https://doi.org/10.1109/IPDPS.2010.5470407>`_

Hines, M., Davison, A. P., Muller, E. (2009). NEURON and Python. *Frontiers in neuroinformatics*, 3, 1. `doi:10.3389/neuro.11.001.2009 <https://doi.org/10.3389/neuro.11.001.2009>`_

Davison, A. P., Hines, M., Muller, E. (2009). Trends in programming languages for neuroscience simulations. *Frontiers in neuroscience*, 3, 36. `doi:10.3389/neuro.01.036.2009 <https://doi.org/10.3389/neuro.01.036.2009>`_

Hines, M. L., Markram, H., Schürmann, F. (2008). Fully implicit parallel simulation of single neurons. *Journal of computational neuroscience*, 25(3), 439-448. `doi:10.1007/s10827-008-0087-5 <https://doi.org/10.1007/s10827-008-0087-5>`_

Hines, M. L., Eichner, H., Schürmann, F. (2008). Neuron splitting in compute-bound parallel network simulations enables runtime scaling with twice as many processors. *Journal of computational neuroscience*, 25(1), 203-210. `doi:10.1007/s10827-007-0073-3 <https://doi.org/10.1007/s10827-007-0073-3>`_

Carnevale NT, Hines M. (2008). The NEURON simulation environment in epilepsy research. In *Computational Neuroscience in Epilepsy* (pp. 18-33). Academic Press. `doi:/10.1016/B978-012373649-9.50005-3 <https://doi.org/10.1016/B978-012373649-9.50005-3>`_

Lytton, W. W., Stewart, M., Hines, M. (2008). Simulation of large networks: technique and progress. In *Computational neuroscience in epilepsy* (pp. 3-17). Academic Press. `doi:10.1016/B978-012373649-9.50004-1 <https://doi.org/10.1016/B978-012373649-9.50004-1>`_

Carnevale NT, Hines ML. (2008). Translating network models to parallel hardware in NEURON. *Journal of neuroscience methods*, 169(2), 425. `doi:10.1016/j.jneumeth.2007.09.010 <https://doi.org/10.1016/j.jneumeth.2007.09.010>`_

Cannon, R. C., Gewaltig, M. O., Gleeson, P., Bhalla, U. S., Cornelis, H., Hines, M. L., ...  De Schutter, E. (2007). Interoperability of neuroscience modeling software: current status and future directions. *Neuroinformatics*, 5(2), 127-138. `doi:10.1007/s12021-007-0004-5 <https://doi.org/10.1007/s12021-007-0004-5>`_

Hines ML, Morse TM, Carnevale NT (2007). Model structure analysis in NEURON (2007). In Crasto CJ. (Ed) *Methods in Molecular Biology, vol 401: Neuroinformatics.* Humana Press Inc., Totowa, NJ. `doi:10.1007/978-1-59745-520-6 <https://doi.org/10.1007/978-1-59745-520-6>`_

Brette, R., Rudolph, M., Carnevale, T., Hines, M., Beeman, D., Bower, J. M., ...  Destexhe, A. (2007). Simulation of networks of spiking neurons: a review of tools and strategies. *Journal of computational neuroscience*, 23(3), 349-398. `doi:10.1007/s10827-007-0038-6 <https://doi.org/10.1007/s10827-007-0038-6>`_

Carnevale NT, Hines ML. (2006). *The NEURON book*. Cambridge University Press. `doi:10.1017/CBO9780511541612 <https://doi.org/10.1017/CBO9780511541612>`_

Migliore, M., Cannia, C., Lytton, W. W., Markram, H., Hines, M. L. (2006). Parallel network simulations with NEURON. *Journal of computational neuroscience*, 21(2), 119-129. `doi:10.1007/s10827-006-7949-5 <https://doi.org/10.1007/s10827-006-7949-5>`_

Lytton, W. W., Hines, M. L. (2005). Independent variable time-step integration of individual neurons for network simulations. *Neural computation*, 17(4), 903-921. `doi:10.1162/0899766053429453 <https://doi.org/10.1162/0899766053429453>`_

Hines M, Carnevale N. (2005). Recent developments in neuron. *Brains, Minds and Media*, 1(2). `www.brains-minds-media.org/archive/221/bmm221.pdf <https://www.brains-minds-media.org/archive/221/bmm221.pdf>`_

    Introduces: The Channel Builder, The Cell Builder, ModelView, and the Import3D tool.

Hines ML, Carnevale NT. (2004). Discrete event simulation in the NEURON environment. *Neurocomputing*, 58, 1117-1122. `doi:10.1016/j.neucom.2004.01.175 <https://doi.org/10.1016/j.neucom.2004.01.175>`_

Hines, M. L., & Carnevale, N. (2003). The NEURON simulation environment. In: *The Handbook of Brain Theory and Neural Networks*. MIT Press, Cambridge, MA, USA.

Hines ML, Carnevale NT. (2001). NEURON: a tool for neuroscientists. *The neuroscientist*, 7(2), 123-135. `doi:10.1177/107385840100700207 <https://doi.org/10.1177/107385840100700207>`_

Hines ML, Carnevale NT. (2000). Expanding NEURON's repertoire of mechanisms with NMODL. *Neural computation*, 12(5), 995-1007. `doi:10.1162/089976600300015475 <https://doi.org/10.1162/089976600300015475>`_

Shepherd, G. M., Mirsky, J. S., Healy, M. D., Singer, M. S., Skoufos, E., Hines, M. S., ... Miller, P. L. (1998). The Human Brain Project: neuroinformatics tools for integrating, searching and modeling multidisciplinary neuroscience data. *Trends in neurosciences*, 21(11), 460-468. `doi:10.1016/S0166-2236(98)01300-9 <https://doi.org/10.1016/S0166-2236(98)01300-9>`_

Hines, M. L. (1998). The neurosimulator NEURON. Methods in neuronal modeling: from synapses to networks (Koch C, Segev I, eds), 121-136. MIT Press. Cambridge, MA.

Hines ML, Carnevale NT. (1997). The NEURON simulation environment. *Neural computation*, 9(6), 1179-1209. `doi:10.1162/neco.1997.9.6.1179 <https://doi.org/10.1162/neco.1997.9.6.1179>`_

Lytton, W. W., Contreras, D., Destexhe, A., & Steriade, M. (1997). Dynamic interactions determine partial thalamic quiescence in a computer network model of spike-and-wave seizures. *Journal of Neurophysiology*, 77(4), 1679-1696. `doi:10.1152/jn.1997.77.4.1679 <https://doi.org/10.1152/jn.1997.77.4.1679>`_

Lytton WW. (1997). Brain organization: from molecules to parallel processing. In *Contemporary Behavioral Neurology*, M. R. Trimble and J. L. Cummings, eds., pp. 5–28. Butterworth-Heinemann, Newton, MA.

Hines M. (1994). The NEURON simulation program. In: *Neural network simulation environments* (pp. 147-163). Springer, Boston, MA. `link.springer.com/chapter/10.1007/978-1-4615-2736-7_8 <https://link.springer.com/chapter/10.1007/978-1-4615-2736-7_8>`_

Hines M. (1993). NEURON -- a program for simulation of nerve equations. In: Eeckman F.H. (ed) *Neural Systems: Analysis and Modeling*. Springer, Boston, MA. `doi:10.1007/978-1-4615-3560-7_11 <https://doi.org/10.1007/978-1-4615-3560-7_11>`_

Hines M. (1989). A program for simulation of nerve equations with branching geometries. *International journal of bio-medical computing*, 24(1), 55-68. `doi:10.1016/0020-7101(89)90007-X <https://doi.org/10.1016/0020-7101(89)90007-X>`_


Hines, M. (1984). Efficient computation of branched nerve equations. *International journal of bio-medical computing*, 15(1), 69-76. `doi:10.1016/0020-7101(84)90008-4 <https://doi.org/10.1016/0020-7101(84)90008-4>`_
